DNA methylation, the addition of a methyl group to the carbon-5 position of cytosine residues, is the only common covalent modification of human DNA and occurs almost exclusively at cytosines that are followed immediately by a guanine (so-called CpG dinucleotides). The bulk of the genome displays a clear depletion of CpG dinucleotides, and those that are present are nearly always methylated. By...

More than 50% of mammalian genes are associated with CpG islands and thus they serve as a good gene marker. We have devised a simple method to scan large pieces of native or cloned genomic DNA for CpG islands. The method is based on the presence of multiple Hpa II and Hha I sites in CpG islands, at a frequency 30 times higher than in the rest of the genome. The steps include complete digestion ...

dna methylation is an important biological process involving in human disease such as cancer insomia and diabetes. bisulfite sequencing (bs-seq) with next-generation technology is an accurate method for measuring dna methylation. bs-seq data analysis is a considerable way to recognize methylated cytosines and several tools have been developed to analysis bs-seq such as bs-seeker, b-solana, brat...

ARHI is a maternally imprinted tumor suppressor gene that maps to a site on chromosome 1p31 where loss of heterozygosity has been observed in 40% of human breast and ovarian cancers. ARHI is expressed in normal ovarian and breast epithelial cells, but ARHI expression is lost in a majority of ovarian and breast cancers. Expression of ARHI from the paternal allele can be down-regulated by multipl...

We have investigated the accessibility of the 5' CpG rich sequences (CpG islands) present in the 5' region of most if not all HLA class I genes to methylation sensitive rare cutter enzymes. We show that for HLA-A, -B, -C genes and a few other (but not all) class I sequences these CpG islands are unmethylated and therefore constitute HTF islands (CpG rich, unmethylated regions of DNA, usually as...

DNA methyltransferase (DNMT) inhibitors are epigenetic drugs used to treat myelodysplastic syndrome. They not only induce DNA demethylation but also have significant cytostatic and cytotoxic effects; however, the relationships between these characteristics have not been established yet due to the lack of a method to induce only DNA demethylation. Herein, we show that a fusion protein comprised ...

Although most CpG islands are generally thought to remain unmethylated in all adult somatic tissues, recent genome-wide approaches have found that some CpG islands have distinct methylation patterns in various tissues, with most differences being seen between germ cells and somatic tissues. Few studies have addressed this among human somatic tissues and fewer still have studied the same sets of...

CpG islands are distinguishable from the bulk of vertebrate DNA for being unmethylated and CpG-rich. Since CpG doublets are the specific target of eukaryotic DNA methyltransferases, CpG-rich sequences might be expected to be good methyl-accepting substrates in vitro, despite their unmethylated in vivo condition. This was tested using a partially purified DNA-methyltransferase from human placent...

The duplication of mammalian genomes is under the control of a spatiotemporal program that orchestrates the positioning and the timing of firing of replication origins. The molecular mechanisms coordinating the activation of about [Formula: see text] predicted origins remain poorly understood, partly due to the intrinsic rarity of replication bubbles, making it difficult to purify short nascent...

Aberrant DNA methylation patterns may be the earliest somatic genome changes in prostate cancer. Using real-time methylation-specific PCR, we assessed the extent of hypermethylation at 16 CpG islands in DNA from seven prostate cancer cell lines (LNCaP, PC-3, DU-145, LAPC-4, CWR22Rv1, VCaP, and C42B), normal prostate epithelial cells, normal prostate stromal cells, 73 primary prostate cancers, 9...